Light energy fluorescence excitation

ABSTRACT

There is set forth herein a light energy exciter that can include one or more light sources. A light energy exciter can emit excitation light directed toward a detector surface that can support biological or chemical samples.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims priority to U.S. Patent Application No.62/611,448, filed Dec. 28, 2017, entitled, “Light Energy FluorescenceExcitation,” which is incorporated herein by reference in its entirety.This application also claims priority to U.S. Patent Application No.62/644,805, filed Mar. 19, 2018, entitled, “Light Energy FluorescenceExcitation,” which is incorporated herein by reference in its entirety.This application also claims priority to Dutch Patent Application No.2020636, filed Mar. 20, 2018, entitled, “Light Energy FluorescenceExcitation,” which is incorporated herein by reference in its entirety.

BACKGROUND

Various protocols in biological or chemical research involve performingcontrolled reactions. The designated reactions can then be observed ordetected and subsequent analysis can help identify or reveal propertiesof chemicals involved in the reaction.

In some multiplex assays, an unknown analyte having an identifiablelabel (e.g., fluorescent label) can be exposed to thousands of knownprobes under controlled conditions. Each known probe can be depositedinto a corresponding well of a microplate. Observing any chemicalreactions that occur between the known probes and the unknown analytewithin the wells can help identify or reveal properties of the analyte.Other examples of such protocols include known DNA sequencing processes,such as sequencing-by-synthesis (SBS) or cyclic-array sequencing.

In some fluorescent-detection protocols, an optical system is used todirect excitation light onto fluorophores, e.g. fluorescently-labeledanalytes and to also detect the fluorescent emissions signal light thatcan emit from the analytes having attached fluorophores. However, suchoptical systems can be relatively expensive and require a largerbenchtop footprint. For example, the optical system can include anarrangement of lenses, filters, and light sources.

In other proposed detection systems, the controlled reactions in a flowcell define by a solid-state light sensor array (e.g. a complementarymetal oxide semiconductor (CMOS) detector or a charge coupled device(CCD) detector). These systems do not involve a large optical assemblyto detect the fluorescent emissions.

BRIEF DESCRIPTION

There is set forth herein a light energy exciter that can include one ormore light sources. A light energy exciter can emit excitation lightdirected toward a detector surface that can support biological orchemical samples.

There is set forth herein a method comprising: emitting with a lightenergy exciter excitation light, wherein the light energy excitercomprises a first light source and a second light source, the firstlight source to emit excitation light rays in a first wavelengthemission band, the second light source to emit excitation light rays ina second wavelength emission band; and receiving with a detector theexcitation light and emissions signal light resulting from excitation bythe excitation light, the detector comprising a detector surface forsupporting biological or chemical samples and a sensor array spacedapart from the detector surface, the detector blocking the excitationlight and permitting the emissions signal light to propagate towardlight sensors of the sensor array; and transmitting with circuitry ofthe detector data signals in dependence on photons sensed by the lightsensors of the sensor array.

There is set forth herein a light energy exciter comprising: at leastone light source to emit excitation light rays; and a light pipehomogenizing the excitation light and directing the excitation lighttoward a distal end of the light energy exciter, the light pipecomprising a light entrance surface and a light exit surface, the lightpipe receiving the excitation light rays from the at least one lightsource; wherein the distal end of the light energy exciter is adaptedfor coupling with a detector assembly that comprises a detector surfacefor supporting biological or chemical samples.

There is set forth herein a system comprising: a light energy excitercomprising at least one light source to emit excitation light rays, anda light pipe to homogenize the excitation light rays and to direct theexcitation light rays, the light pipe comprising a light entrancesurface to receive the excitation light rays from the at least one lightsource; and a detector comprising a detector surface for supportingbiological or chemical samples and a sensor array comprising lightsensors spaced apart from the detector surface, wherein the detectorreceives excitation light from the exciter and emissions signal light,wherein the detector comprises circuitry to transmit data signals independence on photons detected by light sensors of the sensor array,wherein the detector blocks the excitation light and permits theemissions signal light to propagate toward the light sensors.

It should be appreciated that all combinations of the foregoing conceptsand additional concepts discussed in greater detail below (provided suchconcepts are not mutually inconsistent) are contemplated as being partof the inventive subject matter disclosed herein. In particular, allcombinations of claimed subject matter appearing at the end of thisdisclosure are contemplated as being part of the inventive subjectmatter disclosed herein.

DRAWINGS

These and other features, aspects, and advantages set forth herein willbecome better understood when the following detailed description is readwith reference to the accompanying drawings in which like charactersrepresent like parts throughout the drawings, wherein:

FIG. 1 is a schematic block diagram of a system for performance ofbiological or chemical tests, the system having a light energy exciterand a detector assembly having a detector according to one example;

FIG. 2 is a cutaway side view of a light energy exciter according to oneexample;

FIG. 3 is a ray trace diagram illustrating light ray propagation in thelight energy exciter of FIG. 2 according to one example;

FIG. 4 depicts a light source bank including light sources provided by aplurality of LEDs disposed on a printed circuit board according to oneexample;

FIG. 5 is a side view of light sources provided by a plurality of LEDssurface coupled onto a light entry surface of a light pipe according toone example;

FIG. 6 is a perspective schematic view of a light energy exciteraccording to one example;

FIG. 7 is a schematic diagram of a light energy exciter according to oneexample;

FIG. 8 is a ray trace diagram illustrating operation of a light energyexciter having first and second light pipes according to one example;

FIG. 9 is a perspective cutaway side view showing a light energy exciteraccording to one example;

FIG. 10 is a perspective view of a system having a light energy excitercoupled with a detector assembly according to one example;

FIG. 11 is an assembly perspective view of a flow cell frame defining aflow cell according to one example;

FIG. 12 is an internal view of a detector assembly cartridge definingregistration features for alignment of a light energy exciter that canbe coupled and aligned thereon according to one example;

FIG. 13 is a top view of the flow cell defined with respect to adetector provided by an integrated circuit according to one example;

FIG. 14 is a light energy exciter provided by a single piece of materialdefining a light pipe and a lens according to one example;

FIG. 15 is a perspective view of a light energy exciter having a singlepiece of material that commonly defines a light pipe and a lens, whereinthe lens is provided by a Fresnel lens according to one example;

FIG. 16 is a cutaway side view of a portion of a detector provided by anintegrated circuit having a light sensor array and an aligned lightguide array according to one example;

FIG. 17 is a cutaway side view of a portion of a detector provided by anintegrated circuit having a light sensor and an aligned light guideaccording to one example;

FIG. 18 is a schematic diagram of a process control system according toone example,

FIG. 19 is a spectral profile coordination diagram depicting spectralprofiles of a plurality of light energy exciter light sources and aplurality of fluorophores that may be excited with use of the excitationlight sources; and

FIG. 20 is a flowchart depicting process that can be used in support ofa DNA sequencing process for DNA sequence reconstruction.

DETAILED DESCRIPTION

In FIG. 1 there is set forth a light energy exciter 10 for use in asystem 100. System 100 can be used to perform biological or chemicaltests. System 100 can include light energy exciter 10 and detectorassembly 20. Detector assembly 20 can include detector 200 and flow cell282. Detector 200 can include a plurality of light sensors 202 anddetector surface 206 for supporting samples 502 e.g. analytes which canbe provided by DNA fragments. Detector surface 206 according to oneexample can define a plurality of reaction recesses 210 and samples 502such as biological or chemical samples can be supported within suchreaction recesses 210.

Detector 200 can include a plurality of light guides 214 that receiveexcitation light and emissions signal light from detector surface 206resulting from excitation by the excitation light. The light guides 214can guide light from detector surface 206. The light guides 214 extendtoward respective light sensors 102 and can include filter material thatblocks the excitation light and permits the emissions signal light topropagate toward the respective light sensors.

According to one example, detector 200 can be provided by a solid-stateintegrated circuit detector such as a complementary metal oxidesemiconductor (CMOS) integrated circuit detector or a charge coupleddevice (CCD) integrated circuit detector.

According to one example, each light sensor 202 can be aligned to arespective light guide 214 and a respective reaction recess 210 so thatlongitudinal axis 268 extends through a cross sectional geometric centerof a light sensor 202, light guide 214 and reaction recess 210. Flowcell 282 can be defined by detector surface 206, sidewalls 284, and flowcover 288. Flow cover 288 can be a light transmissive cover to transmitexcitation light provided by light energy exciter 10.

In another aspect, detector 200 can include dielectric stack areas 218,intermediate of the light guides 214. Dielectric stack areas 218 canhave formed therein circuitry, e.g. for read out of signals from lightsensors 202 digitization storage and processing.

System 100 can include inlet portal 289 through which fluid can enterflow cell 282 and outlet portal 290 through which fluid can exit flowcell 282. Inlet portal 289 and outlet portal 290 can be defined by flowcover 288.

According to one example, system 100 can be used for performance ofbiological or chemical testing with use of fluorophores. For example, afluid having one or more fluorophore can be caused to flow into and outof flow cell 282 through inlet port using inlet portal 289 and outletportal 290. Fluorophores can attract to various samples 502 and thus, bytheir detection fluorophores can act as markers for the samples 502 e.g.biological or chemical analytes to which they attract.

To detect the presence of a fluorophore within flow cell 282, lightenergy exciter 10 can be energized so that excitation light 101 in anexcitation wavelength range is emitted by light energy exciter 10. Onreceipt of excitation light fluorophores attached to samples 502 canradiate emissions signal light 501 which is the signal of interest fordetection by light sensors 202. Emissions signal light 501 owing tofluorescence of a fluorophore attached to a sample 502 will have awavelength range red shifted relative to a wavelength range ofexcitation light 101.

Light energy exciter 10 can be activated to emit excitation light 101 toexcite fluorophores that have attached to samples 502. On being excitedby excitation light 101 fluorophores attached to samples 5102 canfluoresce to radiate emissions signal light 501 at a wavelength rangehaving longer wavelengths than a wavelength range of excitation light101. The presence or absence of emissions signal light 501 can indicatea characteristic of a sample 502. Light guides 214 according to oneexample can filter light in the wavelength range of excitation light 101transmitted by light energy exciter 10 so that light sensors 202 do notdetect excitation light 101 as emissions signal light 501.

System 100 in test support systems area 300 can include process controlsystem 310, fluid control system 320, fluid storage system 330, and userinterface 340 which permits an operator to enter inputs for control ofsystem 100. Process control system 310 according to one example can beprovided by processor based system. Process control system 310 can runvarious biological or chemical processes such as DNA sequencereconstruction processes. According to one example, for running of abiological or chemical process, process control system 310 can sendcoordinated control signals e.g. to light energy exciter 10, detector200 and/or fluid control system 320. Fluid storage system 330 can storefluids that flow through flow cell 282.

According to one example, light energy exciter 10 can include one ormore light sources. According to one example, light energy exciter 10can include one or more light shaping element. Light energy exciter 10can include one or more optical component for shaping light emissionsdirecting light emitted from the one or more light sources. The one ormore light sources can include, e.g. one or more light pipe, lens,wedge, prism, reflector, filter, grating, collimator, or any combinationof the above.

FIG. 2 illustrates a light energy exciter 10 according to one example.Light energy exciter 10 can include a light source bank 102 having oneor more light sources, e.g. light source 102A-102Z and various opticalelements for directing light along optical axis 106, which in theexample shown is a folded axis.

Light energy exciter 10 can include light pipe 110 and lens 114 forshaping excitation light rays transmitted through light pipe 110. Lightpipe 110 and lens 114 can have cross sectional geometric centerscentered on optical axis 106.

Light pipe 110 can include light entry surface 109 and light exitsurface 111. Excitation light 101 emitted from light source bank 102 canenter light entry surface 109 and can exit light exit surface 111 oflight pipe 110. Light pipe 110 by having an index of refraction selectedfor providing internal reflections can reflect received light raysreceived from light source bank 102 in various directions to homogenizelight so that exit light rays transmitted through light pipe 110 arehomogenous. Thus, even where a light source of light source bank 102 mayhave “hot spots” or is asymmetrically disposed with respect to lightpipe 110 or have other irregularities, homogenous light can be producedat the light exit surface 111 of light pipe 110.

Light pipe 110 by having an index of refraction selected for providinginternal reflections can confine excitation light rays that it receivesand transmits to the volumetric area delimited by sidewall surfacesdefining light pipe 110. Light pipe 110 can be formed of homogenouslight transmissive material, e.g. polycarbonate or silica glass.

According to one example, light pipe 110 can be of tapered constructiondefined by an increasing diameter throughout its length in a directionfrom the light entry surface 109 to the light exit surface 111 of lightpipe 110. According to one example, light pipe 110 can be of taperedconstruction defined by a linearly increasing diameter throughout itslength in a direction from the light entry surface 109 to the light exitsurface 111 of light pipe 110.

According to one example, light energy exciter 10 can be configured sothat lens 114 images light exit surface 111 of light pipe 110 onto imageplane 130 and according to one example system 100 can be configured sothat image plane 130 coincides with detector surface 206 which can beconfigured to support a sample 502 such as a DNA fragment. Lens 114 byimaging an object plane onto an image plane can project an image ofhomogenized light present at light exit surface 111 of light pipe 110onto sample supporting detector surface 206 of detector 200 (FIG. 1).

Examples herein recognize that while light source bank 102 can beselected so that excitation light rays emitted from light source bank102 do not include fluorescence range light rays, fluorescence rangelight rays can nevertheless radiate within light energy exciter 10 as aresult of autofluorescence. In another aspect, light energy exciter 10can include a short pass filter 122 to filter fluorescence rangewavelengths radiating as a result of autofluorescence from within lightenergy exciter 10, e.g. radiating from lens 114, light pipe 110, andreflector 118 as well as other surfaces of light energy exciter 10

Light energy exciter 10 can include light reflector 118 for foldingoptical axis 106 so that optical axis 106 changes direction from a firstdirection in which optical axis 106 extends parallel to the reference Yaxis shown to a second direction in which optical axis 106 extendsparallel to the reference Z axis shown. Light energy exciter 10 caninclude window 126 having a cross sectional center centered on opticalaxis 106 as well as housing 134 and other supporting components forsupporting the various optical components in certain spatial relationsuch as the certain spatial relation depicted in FIG. 1.

A ray trace diagram for light energy exciter 10 in the example of FIG. 2is shown in FIG. 3. Referring to the ray trace diagram of FIG. 3, lens114 can image an object plane 112 which can be defined at the light exitsurface 111 of light pipe 110 onto an image plane 130 which can belocated at detector surface 206 that can be adapted to supportbiological or chemical samples. As seen from the ray trace diagram ofFIG. 3, light rays exiting light exit surface 111 of light pipe 110 canbe diverging light rays that diverge at a divergence angle that issufficiently restricted so that a majority of light rays exiting lightexit surface 111 of light pipe 110 are received by light entry surfaceof lens 114. Examples herein recognize that while light pipes are usefulfor purposes of homogenizing light, they are capable of transmittingexit light rays that exit at large maximum divergence angles, e.g.approaching 90°.

Examples herein recognize for example that in the case that light pipe110 is constructed alternatively to have a uniform diameter, i.e. anon-tapered diameter, a substantial percentage of exit light raysexiting light pipe 110 may exit light exit surface 111 at a divergenceangle that is sufficiently large that a light entry surface 113 of lens114 may not collect the exit light rays. Examples herein recognize thatproviding light pipe 110 to be of tapered construction, tapered alongits length and having a geometric cross sectional center centered onoptical axis 106 and including an appropriate index of refractionprovides reflections within light pipe 110 so that light exiting lightrays exiting light exit surface 111 of light pipe 110 exit light exitsurface 111 of light pipe 110 at an angle that is reduced relative to a90° angle of maximum divergence.

In the example described in reference to FIGS. 2 and 3, exit light raysexiting light exit surface 111 of light pipe 110 can define a divergingcone of light 1100 having light rays that diverge at angles ranging fromzero degrees to a maximum divergence angle in respect to a referencelight ray extending from the light exit surface in a direction parallelto optical axis 106. The defined diverging cone of light 1100 candiverge at the maximum divergence angle with respect to optical axis106. According to one example, the maximum divergence angle is adivergence angle designed so that the majority of exit light raysexiting light exit surface 111 are collected by a light entry surface oflens 114. According to one example, the light energy exciter 10 isconfigured so that light excitation light rays exiting exit surface 111diverge at a maximum divergence angle respect to a reference light rayextending from the light exit surface in a direction parallel to opticalaxis 106 that is sufficiently small so as to ensure collection by lightentry surface 113 of lens 114.

According to one example, light energy exciter 10 can be configured sothat exit light rays exiting light exit surface 111 of light pipe 110define a diverging cone of light 1100 having light rays that diverge atangles ranging from zero degrees to a maximum divergence angle inrespect to a reference light ray extending from the light exit surfacein a direction parallel to optical axis 106, wherein the light pipe 110is configured so that the maximum divergence angle is about 60 degreesor less. According to one example, light energy exciter 10 is configuredso that exit light rays exiting light exit surface 111 of light pipe 110define a diverging cone of light 1100 having light rays that diverge atangles ranging from zero degrees to a maximum divergence angle inrespect to a reference light ray extending from the light exit surfacein a direction parallel to optical axis 106, wherein the light pipe 110is configured so that the maximum divergence angle is about 50 degreesor less. According to one example, light energy exciter 10 is configuredso that exit light rays exiting light exit surface 111 of light pipe 110define a diverging cone of light 1100 having light rays that diverge atangles ranging from zero degrees to a maximum divergence angle inrespect to a reference light ray extending from the light exit surfacein a direction parallel to optical axis 106, wherein the light pipe 110is configured so that the maximum divergence angle is about 40 degreesor less. According to one example, light energy exciter 10 is configuredso that exit light rays exiting light exit surface 111 of light pipe 110define a diverging cone of light 1100 having light rays that diverge atangles ranging from zero degrees to a maximum divergence angle inrespect to a reference light ray extending from the light exit surfacein a direction parallel to optical axis 106, wherein the light pipe 110is configured so that the maximum divergence angle is about 35 degreesor less. According to one example, light energy exciter 10 is configuredso that exit light rays exiting light exit surface 111 of light pipe 110define a diverging cone of light 1100 having light rays that diverge atangles ranging from zero degrees to a maximum divergence angle inrespect to a reference light ray extending from the light exit surfacein a direction parallel to optical axis 106, wherein the light pipe 110is configured so that the maximum divergence angle is about 30 degreesor less.

For providing imaging functionality, lens 114 can converge receivedexcitation light rays transmitted through light pipe 110. In the exampledescribed in reference to FIGS. 2 and 3, exit light rays exiting lightexit surface 115 of lens 114 can define a converging cone of light 1400having light rays that converge at angles ranging from zero degrees to amaximum convergence angle in respect to a reference light ray extendingfrom the light exit surface in a direction parallel to optical axis 106,wherein the lens 114 is configured so that the maximum convergence angleis about 60 degrees or less. The defined converging cone of light 1400can converge at the maximum convergence angle with respect to opticalaxis 106. In the example described in reference to FIGS. 2 and 3, exitlight rays exiting light exit surface 115 of lens 114 can define aconverging cone of light 1400 having light rays that converge at anglesranging from zero degrees to a maximum convergence angle in respect to areference light ray extending from the light exit surface in a directionparallel to optical axis 106, wherein the lens 114 is configured so thatthe maximum convergence angle is about 50 degrees or less. In theexample described in reference to FIGS. 2 and 3, exit light rays exitinglight exit surface 115 of lens 114 can define a converging cone of light1400 having light rays that converge at angles ranging from zero degreesto a maximum convergence angle in respect to a reference light rayextending from the light exit surface in a direction parallel to opticalaxis 106, wherein the lens 114 is configured so that the maximumconvergence angle is about 40 degrees or less. In the example describedin reference to FIGS. 2 and 3, exit light rays exiting light exitsurface 115 of lens 114 can define a converging cone of light 1400having light rays that converge at angles ranging from zero degrees to amaximum convergence angle in respect to a reference light ray extendingfrom the light exit surface in a direction parallel to optical axis 106,wherein the lens 114 is configured so that the maximum convergence angleis about 35 degrees or less. In the example described in reference toFIGS. 2 and 3, exit light rays exiting light exit surface 115 of lens114 can define a converging cone of light 1400 having light rays thatconverge at angles ranging from zero degrees to a maximum convergenceangle in respect to a reference light ray extending from the light exitsurface in a direction parallel to optical axis 106, wherein the lens114 is configured so that the maximum convergence angle is about 30degrees or less.

FIG. 4 illustrates light source bank 102 according to one example. Lightsource bank 102 can include one or more light sources. According to oneexample, one or more light sources can be provided by one or moreelectroluminescence based light sources, e.g. a light emitting diode, alight emitting electrochemical cell, an electroluminescent wire, or alaser, or any combination of the above. In the example described in FIG.4, light source bank 102 can include a plurality of light sources102A-102J provided by a plurality of light emitting diodes (LEDs). Lightsources 102A-102G in the example described can be green LEDs emittingexcitation light rays in the green wavelength band and light sources102H-102J can be blue LEDs emitting excitation light rays in the bluewavelength band. Light sources 102A-102J provided by LEDs can bedisposed on printed circuit board 1020 according to one example. Inoperation of system 100, process control system 310 can controlenergization of light sources 102A-102J provided by LEDs so that one ormore LEDs of a certain emission band is selectively activated at acertain time. Light sources 102A-102J according to one example can beprovided by surface emitting LEDs. LEDs such as surface emitting LEDscan have emissions patterns that correlate ray angles with lightintensity. LED emissions patterns can be a function of such parametersas a die geometry, a die window, indices of and refraction of lightshaping materials. Emissions patterns can be Lambertian according to oneexample i.e. specifying that intensity is proportional to the cosine ofthe emission angle relative to the normal.

Process control system 310 for example can energize only light sources102A-102G provided by green LEDs during a first exposure period ofdetector 200 in which light sensors 202 are exposed and can energizeonly light sources 102H-102J provided by blue LEDs during a secondexposure period of detector 200 in which light sensors 202 are exposed.Providing light source bank 102 to emit at two independently selectablepeak wavelengths facilities a dye chemistry process that can use bothgreen (532 nm) and blue (470 nm) excitation. According to one example,light source bank 102 can include a light source e.g. a red LED disposedon printed circuit board 1020 that emits at a red band center wavelength(e.g. red: 630 nm). Providing red illumination facilitates additionaltest and calibration procedures according to one example.

It is seen in reference to FIG. 4 that light sources defining lightsource bank 102 need not be arranged symmetrically uniformly oraccording to any ordered configuration. For example, it is seen thataccording to the particular configuration shown in FIG. 4, wherein lightsources 102A-102G provided by green LEDs are selectively energized withlight sources 102H-102J provided by blue LEDs maintained in adeenergized state, a larger percentage of excitation light rays willenter light pipe 110 through a left side of light entry surface 109 oflight pipe 110, and when light sources 102H-102J provided by blue LEDsare selectively energized with green LEDs maintained in a deenergizedstate, a larger percentage of excitation light rays will enter lightpipe through a right side of light entry surface 109 of light pipe 110.

Notwithstanding, light pipe 110 by its light reflective propertieshomogenizes the imbalanced incoming received light to producehomogenized light at the light exit surface 111 of light pipe 110irrespective of the arrangement of light sources of light source bank102. The refractive index of light pipe 110 can be chosen such that thelight rays from light source bank 102 exhibit total internal reflection(TIR) within light pipe 110 such that at light exit surface 111 of lightpipe 110, homogeneous (uniform) illumination is achieved.

As shown in FIG. 5, light source bank 102 can be coupled to light pipe110 in a manner to assure reduced light loss. In the arrangementdepicted in FIG. 5, there is a side view of the LEDs shown as beingdisposed on printed circuit board 1020 in FIG. 4. In the side viewdepicted in FIG. 5, light sources 102A, 102C, and 102E provided by LEDsare shown to correspond to light sources 102A, 102C, and 102E, asdepicted in FIG. 4. Light sources 102A-102J can be provided by LEDshaving flat planar light emission faces depicted as depicted in FIG. 5.Referring to FIG. 5 the flat planar light emission faces of lightsources 102A-102J provided by LEDs (of which light sources 102A, 102C,and 102E are shown in the side view) are surface coupled (butt coupled)onto light entry surface 109 of light pipe 110. Light entry surface 109like the emission surfaces of light sources 102A-102J provided by LEDs,can be flat and planar to assure low light loss when light sources102A-102J provided by LEDs are surface coupled onto light entry surface109. With use of the surface coupling depicted in FIG. 5, couplingefficiency specifying the efficiency of LED light transmission throughlight pipe 110 of 90 percent or greater can be achieved, and accordingto one example 98 percent or higher, which compares favorably tocoupling efficiency of light sources into a lens where couplingefficiency is in dependence on the numerical aperture of the lens.

Further in reference to FIG. 5, it is seen that an entirety of the frontface of each respective light source 102A-102J provided by LEDs isopposed by light entry surface 109 of light pipe 110, thus assuring thata majority of excitation light rays emitted by light sources 102A-102Jprovided by LEDs are received by light entry surface 109 of light pipe110.

Light energy exciter 10 can emit excitation light 101 (FIG. 1) at afirst lower wavelength range, e.g. below about 560 nm to excitefluorophores which, in response to the excitation light fluoresce toradiate emissions signal light 501 second wavelength range having longerwavelengths, e.g. including wavelengths longer than about 560 nm.Detector 200 can be configured so that these wavelength range emissionsat longer wavelengths are detected by light sensors 202. Detector 200can include light guides 214 that can be formed of filtering material toblock light in the wavelength range of excitation light 101 so thatemissions signal light 501 attributable to fluorescing fluorophores isselectively received by light sensors 202.

Examples herein recognize that if light energy exciter 10 emits light ina fluorescence emission band (fluorescence range) such emitted light canbe undesirably be sensed as emissions signal light by light sensors 202.Examples herein include features to reduce the emission of fluorescencerange wavelengths by light energy exciter 10.

As noted, light energy exciter 10 can include short pass filter 122.Short pass filter 122 permits transmission of excitation light rays inthe emission energy band of light source bank 102 but which blocks lightat a fluorescence range within flow cell 282 attributable toautofluorescing components within light energy exciter 110. Short passfilter 122 can be disposed at a distal end of light energy exciter 10 sothat-short pass filter 122 can reject autofluorescence range wavelengthsattributable to autofluorescing materials within light energy exciter10. To facilitate filtering of autofluorescence range radiationradiating from lens 112 and from components disposed before lens 114 inthe direction of light propagation short pass filter 122 can be disposedafter lens 114 in a light propagation direction at a distal end of lightenergy exciter 10. Short pass filter 122 according to one example caninclude a substrate having deposited thereon alternating layers ofmaterials having higher and lower indices of refraction. Higher index ofrefraction material can include e.g. titanium dioxide (TiO₂) or tantalumpentoxide (Ta₂O₅) and lower index of refraction material can includee.g. silicon dioxide (SiO₂). Material layers can be hard coated e.g.using ion beam sputtering, according to one example.

To further reduce fluorescence range light, materials of light energyexciter 10 can be selected for reduced autofluorescence. Examples hereinrecognize that silicate glass autofluoresces less than polycarbonatematerials commonly used in optical systems. According to one example oneor more optical components of light energy exciter 10 can be selected tobe formed of silicate glass. Examples herein recognize that silicateglass can produce reduced autofluorescence relative to an alternativematerial for optical components and accordingly in accordance with oneexample one or more of light pipe 110, lens 114, short pass filter 122(substrate thereof), and window 126 can be selected to be formed ofsilicate glass for reduction of autofluorescence. According to oneexample one or more of light pipe 110, lens 114, short pass filter 122(substrate thereof), and window 126 is selected to be formed ofhomogeneous silicate glass for reduction of autofluorescence. Accordingto one example each of light pipe 110, lens 114, short pass filter 122(substrate thereof), and window 126 is selected to be formed ofhomogeneous silicate glass for reduction of autofluorescence.

In FIG. 6 a three-dimensional schematic diagram of light energy exciter10 is shown. As shown in FIG. 6, object plane 112 can be imaged by lens114 onto image plane 130. As set forth herein, object plane 112 can bedefined at light exit surface 111 of light pipe 110, so that the imageof the light at light exit surface 111 is projected onto image plane130, which as noted can be located at detector surface 206 (FIG. 1) ofdetector 200 for supporting a sample. It will be understood that becauselens 114 can image the light exit surface 111 of light pipe 110, theshape of the light exit surface 111 can be imaged onto and accordingprojected onto image plane 130. According to one example, the shape oflight exit surface 111 is selected to correspond to the shape and sizeof detector surface 206, and light energy exciter 110 is configured toimage the shape of light exit surface 111 onto image plane 130 so thatlens 114 projects an illumination pattern 107 (FIG. 3) onto detectorsurface 206 that matches a shape and size of detector surface 206.

Configuring light energy exciter 10 to project a light pattern 107 (FIG.3) onto detector surface 206 that matches a shape and size of detectorsurface 206 provides various advantages. By such configuring theprojected illumination pattern does not illuminate areas outside of aperimeter of detector 200 which is wasteful of light energy and alsodoes not under-illuminate areas that are areas of interest.

In the example described with reference to FIG. 6, both light exitsurface 111 and detector surface 206 for supporting a sample can berectilinear in shape. As seen in FIG. 6, light pipe 110 can include arectilinear cross section (taken along 6-6 transverse to optical axis106) throughout its length. Further, as noted, light pipe 110 can be oftapered construction and can have an increasing diameter throughout itslength from light entry surface 109 to light exit surface 111 thereof.Where light pipe 110 has a rectilinear cross section, it will beunderstood that diverging cone of light 1100 defined by excitation lightrays exiting light exit surface 111 of light pipe 110 can have arectilinear cross section with corners becoming softer and more diffusein the direction of light propagation toward light entry surface 113 oflens 114.

According to one example, light energy exciter 10 can be configured sothat light pipe 110 has a rectilinear light exit surface 111, an imageof which can be projected by lens 114 onto detector surface 206 forsupporting a sample which can have a rectilinear shaped perimetercorresponding to a shape of light exit surface 111.

A specification for components of light energy exciter 10 according toone example are set forth FIG. 7 illustrating various optical parametervalues for light energy exciter 10 according to one example. In theexample illustrated in FIG. 7 lens 114 has a 1:1 magnification so that asize of the projected image at the image plane 130 is in common with thesize of the object (the light exit surface 111) at the object plane 112.Light energy exciter 10 according to one example can produce greenillumination intensity of about 5 W/cm{circumflex over ( )}2 at 2A drivecurrent per LED die and blue illumination intensity of about 7W/cm{circumflex over ( )}2 at 2A drive current per LED die. Anillumination uniformity of about >75% can be achieved within the wholeillumination area. Materials for use in light energy exciter 10 are setforth in Table 1 hereinbelow.

TABLE 1 Item Description Property 102 Light source bank SemiLed ®Version 40 mil chips: provided by LEDs Proto; Green: 7 dies; 0.6 W/die;1 × 1 mm²; 525 nm, (±5 nm) Proto; Blue: 3 dies; 1.3 W/die; 1 × 1 mm²;460 nm, (±5 nm) (SemiLed is a trademark of SemiLEDs Optoelectronics Co.,Ltd.) 110 Light pipe Material: N-BK7 ® (N-BK7 is a registered trademarkof SCHOTT Corporation) Length = 35 mm Entrance: 3.3 mm × 4.4 mm; Exit:7.2 mm × 9.1 mm 114 Lens provided Material: Zeonor ® 330R by a lens pairfeff = 20 mm (Zeonor is a registered trademark of Zeon Corporation) 122Filter Semrock ® short pass filter; (Semrock is a registered trademarkof Semrock, Inc.) Substrate Material: Fused Silica; short pass filter λ< 540 nm 126 Window Substrate Material: fused silica Coating: BroadbandDielectric Thickness; 1 mm 118 Reflector provided Substrate Material:N-BK7 ® by a fold mirror (N-BK7 is a registered trademark of SCHOTTCorporation) Coating: Broadband Dielectric

In another example, light pipe 110 can be shaped so that a light exitsurface 111 of light pipe 110 can have a shape other than a rectilinearshape, e.g. can have a circular cross section taken along 6-6 transverseto optical axis 106). Such an example can be advantageous where samplesupporting detector surface 206 has a perimeter that is of a shape otherthan a rectilinear shape and corresponds to the shape of light exitsurface 111.

A design for light energy exciter 10 can be readily be modified foroptimization with different detectors according to detector 200 havingdifferent detector surfaces 206 with different shapes. For example, afirst detector according to detector 200 can have a rectangular shaped(from a top view along Z axis) detector surface 206, a second detectoraccording to detector 200 can have a square shaped detector surface 206,and a third detector according to detector 200 can have a circle shapeddetector surface 206. Because lens 114 is configured to image objectplane 112 coinciding with light exit surface 111 onto detector surface206, light energy exciter 10 can be optimized for use with any of thedifferently shaped detectors simply by changing light pipe 110 to be adifferent configuration. According to one example, as indicated bydashed line 132 of FIG. 2 which indicates a holder for holding aninterchangeable module light energy exciter 10 can be of modularconstruction with a light pipe module 133 being removably exchangeableand light energy exciter 10 can be provided with multiple of such lightpipe blocks modules each with a differently configured one or more lightpipe 110. Optimizing light energy exciter 10 for use with a differentlyshaped detector 200 having a differently shaped detector surface 206 caninclude simply switching out a first currently installed light pipemodule 133 having a first light pipe 110 and first pipe light exitsurface 111 of a first shape with a second light pipe module 133 havinga second light pipe 110 and light pipe exit surface 111 of a secondshape that matches the shape the differently shaped detector 200 havinga differently shaped detector surface 206. Light energy exciter 10 canbe configured so that when a different module is installed into a holderof housing 114 as indicated by dashed line 132, the light exit surface111 of a light pipe 110 of the newly installed module 133 is located onthe object plane 112 so that the light exit surface 111 of light pipe110 can be imaged onto image plane located on detector surface 206.

In the example of FIG. 8 light energy exciter 10 can include light pipe110 as set forth herein and second light pipe 10B. Light pipe 110 can besurface coupled to a first light source 102A, e.g. provided by an LEDand light pipe 110B can be surface coupled to a second light source102B, e.g. provided by second LED. Light source 102A and light source102B can be configured to emit light in the same wavelength band ordifferent wavelength bands. Lens 114 can be configured to image objectplane 112 defined at light exit surface 111 of light pipe 110 and secondlight pipe 110B onto image plane 130 which can be defined on detectorsurface 206. Thus, light energy exciter 10 can project two separateillumination patterns 107A and 107B onto detector surface 206, which canbe advantageous in the case a biological or chemical test designerwishes to separate a detector surface 206 into separate test areas.According to one example, a test designer can specify that a test is tobe performed using a first detector according to detector 200 and asecond detector according to detector 200 and system 100 can beconfigured so that light energy exciter 10 projects the illuminationareas 107 and 17B onto separate detector surfaces 206 respectively ofthe first and second different detectors 200.

There is set forth herein a light energy exciter 10, having a lightsource 102A and a second light source 102B, wherein the light pipe 110receives excitation light from the light source 102A, and wherein theexciter comprises a second light pipe 110B housed in a common housing134 with the light pipe 110, wherein the second light pipe 110B receivethe excitation light from the second light source 102B, wherein thelight pipe 110 and the second light pipe 110B propagate the excitationlight emitted from the first light source 102A and the second lightsource 102B, respectively, and wherein the light energy exciter 10shapes the excitation light propagating, respectively, through the lightpipe 110 and the second light pipe 110B to define first and secondseparate illumination areas 107 and 107B.

The configuration as shown in FIG. 8 can define an optical axis 106 anda second optical axis 106B. In the single channel system as set forth inFIGS. 2-7, optical axis 106 can be co-located with a central axis 1060of lens 114. In the example of FIG. 8 each of optical axis 106 andoptical axis 106B can be offset and parallel to central axis 1060 oflens 114. Each of light pipe 110 and light pipe 110B can define adiverging cone of light 1100 and 1100B respectively having thedivergence angle characteristics of diverging cone of light 1100described with reference to the ray trace diagram (single channelsystem) described with reference to FIG. 3. Lens 114 can definerespective converging cones of light 1400 and 1400B having theconvergence angle characteristics of converging cone of light 1400described with reference to the ray trace diagram (single channelsystem) described with reference to FIG. 3.

According to one example, light pipe 110 and light pipe 110B fordefining first and second illumination channels can be included in a setof interchangeable modules 133 as set forth herein that can beinterchangeably installed into a defined holder of housing 134 of lightenergy exciter 10 indicated by dashed line 132 described in connectionwith FIG. 2.

FIG. 9 illustrates a cutaway physical form view of light energy exciter10. As shown in FIG. 9, light energy exciter 10 can be mounted on a heatsink 702 for drawing heat away from light energy exciter 10 to improvethe performance of light energy exciter 10. FIG. 10 is a perspectivephysical form view of system 100 having light energy exciter 10 coupledto detector assembly 20. As shown in FIG. 10 detector assembly 20 caninclude cartridge 802 that houses flow cell 282. Flow cell 282 can bedefined by flow cell frame 902, as shown in FIG. 11, illustrating aperspective assembly physical form view of flow cell frame 902 definingflow cell 282. Flow cell frame 902 for example can include sidewalls 284and flow cover 288 as depicted in the schematic view of FIG. 1.

FIG. 12 illustrates construction detail illustrating internal componentsof cartridge 802 of detector assembly 20. Cartridge 802 as shown in FIG.12 can be configured to include physical registration features 806 whichaid in the alignment of light energy exciter 10 to detector 200. Asshown in FIG. 2, detector 200 is shown as being located in a locationthat is established by flow cell frame 902 having detector 200 and flowcell 282 received into slot 814 of cartridge 802. Physical registrationfeatures 806 can be provided to catch corresponding features of lightenergy exciter 10 that are defined by a distal end portion of housing134 of light energy exciter 10. For coupling light energy exciter 10 todetector assembly 20 and detector 200, a distal end portion of housing134 of light energy exciter 10 can be inserted into receptacle 826 ofcartridge 802 of detector assembly 20 and arranged so that at a distalend of housing 134 of light energy exciter 10 is registered withcorresponding registration features 806 as shown in FIG. 12 so thatlight energy exciter 10 is properly aligned with flow cell 282 anddetector 200 as shown in FIG. 1.

FIG. 13 illustrates a top view of a flow cell 282 disposed over detector200. According to one example as shown in FIG. 13 flow cell 282 caninclude sidewalls 283 that shape flow cell 282 so that less than alllight sensors 202 are active during a biological or chemical test.Detector 200 according to one example can include an array of 14M oflight sensors which can be regarded as pixels and flow cell 282 can beconfigured by flow cell walls 283 so that about 8M of light sensors 202are active during a biological or chemical test.

Alternative examples of light energy exciter 10 are described withreference to FIGS. 14 and 15. According to one example as shown in FIG.14, lens 114 can be formed integral with light pipe 110. FIG. 14illustrates light pipe 110 and lens 114 integrally formed by a singlepiece of material defining both light pipe 110 and lens 114. Lightenergy exciter 10 can be configured so that lens 114 integrally formedwith light pipe 110 projects homogenized light onto an image plane 130which can be defined at detector surface 206 for supporting a sample(FIG. 1).

FIG. 15 illustrates another example of light energy exciter 10 having anintegrated lens 114 that is integrally formed with light pipe 110 anddefined with a single piece of material that commonly defines both lens114 and light pipe 110. In the example of FIG. 15 lens 114 is shown asbeing provided by a Fresnel lens. Fresnel lenses can produce converginglight rays with reduced lens thicknesses and therefore can provide spacesaving advantages. Lens 114 in the example of FIG. 13 can projecthomogenized light reflected within light pipe 110 onto image plane 130which can be defined at sample supporting detector surface 206. In anyexample herein, including the example of FIGS. 14 and 15 a filtercoating can be directly deposited at the light exit surface 115 of lens114 to remove a discrete filter 22 of light energy exciter 10.

FIGS. 16 and 17 illustrate further details of detector assembly 20 anddetector 200 according to one example that can be used with light energyexciter 10.

In the illustrated example shown in FIG. 16, flow cell 282 is defined bydetector surface 206 sidewall 284 and a flow cover 288 that is supportedby the sidewall 284 and other sidewalls (not shown). The sidewalls canbe coupled to the detector surface 206 and can extend between the flowcover 288 and the detector surface 206. In some examples, the sidewallsare formed from a curable adhesive layer that bonds the flow cover 288to detector 200.

The flow cell 282 can include a height H1. By way of example only, theheight H1 can be between about 50 μm to about 400 μm or, moreparticularly, about 80 μm to about 200 μm. The flow cover 288 caninclude a material that is light transmissive to excitation light 101propagating from an exterior of the detector assembly 20 into the flowcell 282.

Also shown, the flow cover 288 can define inlet portal 289 and outletportal 290 that are configured to fluidically engage other ports (notshown). For example, the other portals can be from a cartridge (notshown) or a workstation (not shown).

Detector 200 can include a sensor array 201 of light sensors 202, aguide array 213 of light guides 214, and a reaction array 209 ofreaction recesses 210. In certain examples, the components are arrangedsuch that each light sensor 202 aligns with a single light guide 214 anda single reaction recess 210. However, in other examples, a single lightsensor 202 can receive photons through more than one light guide 214. Insome examples there can be provided more than one light guide and/orreaction recess for each light sensor of a light sensor array.

In some examples there can be provided more than one light guide and/orlight sensors aligned to a reaction recess of a reaction recess array.The term “array” does not necessarily include each and every item of acertain type that the detector 200 can have. For example, the sensorarray 201 of light sensors 202 may not include each and every lightsensor of detector 200. As another example, the guide array 213 may notinclude each and every light guide 214 of detector 200. As anotherexample, the reaction array 209 may not include each and every reactionrecess 210 of detector 200. As such, unless explicitly recitedotherwise, the term “array” may or may not include all such items ofdetector 200.

Detector 200 has a detector surface 206 that can be functionalized(e.g., chemically or physically modified in a suitable manner forconducting designated reactions). For example, the detector surface 206can be functionalized and can include a plurality of reaction siteshaving one or more biomolecules immobilized thereto. The detectorsurface 206 can have a reaction array 209 of reaction recesses 210. Eachof the reaction recesses 210 can include one or more of the reactionsites. The reaction recesses 210 can be defined by, for example, anindent or change in depth along the detector surface 206. In otherexamples, the detector surface 206 can be substantially planar.

FIG. 17 is an enlarged cross-section of detector 200 showing variousfeatures in greater detail. More specifically, FIG. 17 shows a singlelight sensor 202, a single light guide 214 for directing emissionssignal light 501 toward the light sensor 202, and associated circuitry246 for transmitting signals based on emissions signal light 501 (e.g.,photons) detected by the light sensor 202. It is understood that theother light sensors 202 of the sensor array 201 (FIG. 16) and associatedcomponents can be configured in an identical or similar manner. It isalso understood, however, the detector 200 is not required to bemanufactured identically or uniformly throughout. Instead, one or morelight sensors 202 and/or associated components can be manufactureddifferently or have different relationships with respect to one another.

The circuitry 246 can include interconnected conductive elements (e.g.,conductors, traces, vias, interconnects, etc.) that are capable ofconducting electrical current, such as the transmission of data signalsthat are based on detected photons. Detector 200 comprises an integratedcircuit having a planar array of the light sensors 202. The circuitry246 formed within detector 200 can be configured for at least one ofread out signals from light sensors 202 exposed during an exposureperiod (integration period) in which charge accumulates on light sensors202 in dependence on emission signal light 501 received by light sensors202, signal amplification, digitization, storage, and processing. Thecircuitry 246 can collect and analyze the detected emissions signallight 501 and generate data signals for communicating detection data toa bioassay system. The circuitry 246 can also perform additional analogand/or digital signal processing in detector 200. Light sensors 202 canbe electrically coupled to circuitry 246 through gates 241-243.

Detector 200 according to one example can be provided by a solid-stateintegrated circuit detector such as a CMOS integrated circuit detectoror a CCD integrated circuit detector. Detector 200 according to oneexample can be an integrated circuit chip manufactured using integratedcircuit manufacturing processes such as complementary metal oxidesemiconductor (CMOS) fabrication processes.

The resolution of the sensor array 201 defined by light sensors 202 canbe greater than about 0.5 megapixels (Mpixels). In more specificexamples, the resolution can be greater than about 5 Mpixels and, moreparticularly, greater than about 14 Mpixels.

Detector 200 can include a plurality of stacked layers 231-237 includinga sensor layer 231 which sensor layer 231 can be a silicon layer. Thestacked layers can include a plurality of dielectric layers 232-237. Inthe illustrated example, each of the dielectric layers 232-237 includesmetallic elements (e.g., W (tungsten), Cu (copper), or Al (aluminum))and dielectric material, e.g. SiO₂. Various metallic elements anddielectric material can be used, such as those suitable for integratedcircuit manufacturing. However, in other examples, one or more of thedielectric layers 232-237 can include only dielectric material, such asone or more layers of SiO₂.

With respect to the specific example of FIG. 17, the dielectric layers232-237 can include metallization layers that are labeled as layersM1-M5 in FIG. 17. As shown, the metallization layers, M1-M5, can beconfigured to form at least a portion of the circuitry 246.

In some examples, detector 200 can include a shield structure 250 havingone or more layers that extends throughout an area above metallizationlayer M5. In the illustrated example, the shield structure 250 caninclude a material that is configured to block the light signals thatare propagating from the flow cell 282. The light signals can be theexcitation light 101 and/or emissions signal light 501. By way ofexample only, the shield structure 250 can comprise tungsten (W). By wayof specific example only, the excitation light may have a peakwavelength of about 523 nm (green light) or 456 nm (blue light) andemissions signal light 501 can include wavelengths of about 570 nm andlonger (FIG. 4).

As shown in FIG. 17, shield structure 250 can include an aperture 252therethrough. The shield structure 250 can include an array of suchapertures 252. Aperture 252 can be dimensioned to allow signal emissionlight to propagate to light guide 214. Detector 200 can also include apassivation layer 256 that extends along the shield structure 250 andacross the apertures 252. Detector 200 can also include a passivationlayer 258 comprising detector surface 206 that extends along passivationlayer 256 and across the apertures 252. Shield structure 250 can extendover the apertures 252 thereby directly or indirectly covering theapertures 252. Passivation layer 256 and passivation layer 258 can beconfigured to protect lower elevation layers and the shield structure250 from the fluidic environment of the flow cell 282. According to oneexample, passivation layer 256 is formed of SiN or similar. According toone example, passivation layer 258 is formed of tantalum pentoxide(Ta₂O₅) or similar. Structure 260 having passivation layer 256 andpassivation layer 258 can define detector surface 206 having reactionrecesses 210. Structure 260 defining detector surface 206 can have anynumber of layers such as one to N layer.

Structure 260 can define a solid surface (i.e., the detector surface206) that permits biomolecules or other analytes-of-interest to beimmobilized thereon. For example, each of the reaction sites of areaction recess 210 can include a cluster of biomolecules that areimmobilized to the detector surface 206 of the passivation layer 258.Thus, the passivation layer 258 can be formed from a material thatpermits the reaction sites of reaction recesses 210 to be immobilizedthereto. The passivation layer 258 can also comprise a material that isat least transparent to a desired fluorescent light. Passivation layer258 can be physically or chemically modified to facilitate immobilizingthe biomolecules and/or to facilitate detection of the emissions signallight 501.

In the illustrated example, a portion of the passivation layer 256extends along the shield structure 250 and a portion of the passivationlayer 256 extends directly along filter material defining light guide214. The reaction recess 210 can be aligned with and formed directlyover light guide 214. According to one example each of reaction recess210 and light guide 214 can have cross sectional geometric centerscentered on longitudinal axis 268. Filter material can be deposited in acavity defined by sidewalls 254 formed in a dielectric stack havingstacked layers 232-237.

The light guide 214 can be configured relative to surrounding materialof the dielectric stack defined by dielectric layers 231-237 to form alight-guiding structure. For example, the light guide 214 can have arefractive index of at least about 1.6 according to one example so thatlight energy propagating through light guide 214 is substantiallyreflected at an interface at sidewalls 254 between light guide 214 andthe surrounding dielectric stack defined by dielectric layers 231-237.In certain examples, the light guide 214 can be configured such that theoptical density (OD) or absorbance of the excitation light is at leastabout 4 OD. More specifically, the filter material can be selected andthe light guide 214 can be dimensioned to achieve at least 4 OD. In moreparticular examples, the light guide 214 can be configured to achieve atleast about 5 OD or at least about 6 OD. In more particular examples,the light guide 214 can be configured to achieve at least about 7 OD orat least about 8 OD. Other features of the detector 200 can beconfigured to reduce electrical and optical crosstalk.

In reference to FIG. 18, further details of process control system 310are described. Process control system 310 can include according to oneexample one or more processors 3101, memory 3102, and one or moreinput/output interface 3103. One or more processors 3101, memory 3102and one or more input/output interface can be connected via system bus3104. According to one example process control system 3110 can beprovided by a computer system as set forth in FIG. 18. Memory 3102 caninclude a combination of system memory and storage memory. Memory 3102according to one example can store one or more programs for facilitatingprocesses that are set forth herein. One or more processors 3101 can runone or more programs stored in memory 3102 to facilitate processes as isset forth herein. Memory 3102 can define a computer readable medium.

A DNA sequencing process facilitated by light energy exciter 10 isdescribed with reference to FIGS. 19 and 20. Referring to FIG. 19, thereis shown a spectral profile coordination diagram illustrating aspects ofthe operation of system 100. According to one example light source bank102 can include light sources that emit light at first and seconddifferent wavelengths. Providing light source bank 102 to include lightsources that emit excitation light at first and second differentwavelength ranges facilitates dye chemistry DNA sequence reconstructionprocesses in which first and second dyes can be disposed in fluid withinflow cell 282.

Spectral profile 1702 shown in FIG. 19 illustrates an excitationwavelength emission band of a green emitting light source of lightenergy exciter 10, e.g. such as light source 102A as shown in FIG. 4.Spectral profile 1712 is the wavelength emission band of a blue emittinglight source of light energy exciter 10 such as light source 102H asshown in FIG. 4. Spectral profile 1704 is the absorption band spectralprofile of a first fluorophore sensitive to green light that can bedisposed with fluid into flow cell 282. Spectral profile 1714 is theabsorption band spectral profile of a second fluorophore sensitive toblue light that can be disposed with fluid into flow cell 282. Spectralprofile 1707 is the absorption band spectral profile of a thirdfluorophore sensitive to green light and blue light that can be disposedwith fluid into flow cell 282.

Spectral profile 1706 is the partial spectral profile of emissionssignal light 501 attributable to the first fluorophore fluorescing whenexcited by green light having spectral profile 1702. Spectral profile1716 is the partial spectral profile of emissions signal light 501attributable to the second fluorophore fluorescing when excited by bluelight having spectral profile 1712. Spectral profile 1708 is the partialspectral profile of emissions signal light 501 attributable to the thirdfluorophore fluorescing when excited by green light having spectralprofile 1702. Spectral profile 1709 is the partial spectral profile ofemissions signal light 501 attributable to the third fluorophorefluorescing when excited by blue light having spectral profile 1712.

Spectral profile 1730 is the transmission spectral profile of lightsensors 202 defining light sensor array 201 indicating the detectionband of light sensor array 201.

Examples herein recognize in reference to the spectral profilecoordination diagram of FIG. 19 that process control system 310 can beconfigured to (a) determine that the first fluorophore is attached to asample 502 based on fluorescence being sensed by a light sensor 202under excitation restricted to excitation by one or more green emittinglight sources and fluorescence not being sensed by the light sensor 202under excitation restricted to excitation by one or more blue emittinglight source; (b) determine that the second fluorophore is attached to asample 502 based on fluorescence being sensed by a light sensor 202under excitation restricted to excitation by one or more blue emittinglight sources and fluorescence not being sensed by the light sensor 202under excitation restricted to excitation by one or more green emittinglight sources; and (c) determine that the third fluorophore is attachedto a sample 502 based on fluorescence being sensed by a light sensor 202under excitation restricted to excitation by one or more green emittinglight sources and fluorescence also being sensed by the light sensor 202under excitation restricted to excitation by one or more blue emittinglight sources. Process control system 310 can discriminate whichfluorophores have attached to samples, and can determine nucleotidetypes, e.g. A, C, T, and G that are present in a fragment of a DNAstrand providing a sample 502 e.g. using a decision logic data structureindicated by the decision logic table of Table 2 mapping fluorophorepresence to nucleotide type, where discriminated nucleotidesNucleotide-Nucleotide4 are nucleotides of the nucleotide types A, C, Tand G (the particular mapping based on the test setup parameters).

TABLE 2 Detected fluorescence Detected fluorescence under excitationrestricted under excitation restricted Fluorophore to excitation by oneor more to excitation by one or more presence Nucleotide green emittinglight sources blue emitting light sources indicated indicated YES NOfirst Fluorophore Nucleotide1 NO YES second Fluorophore Nucleotide2 YESYES third Fluorophore Nucleotide3 NO NO — Nucleotide4

Process control system 310 can run a process in support of DNA sequencereconstruction in a plurality of cycles. In each cycle, a differentportion of a DNA fragment can be subject to sequencing processing todetermine a nucleotide type, e.g. A, C, T, or G, associated to thefragment, e.g. using a decision data structure such as a decision datastructure as set forth in Table 2. Aspects of a process which can be runby process control system 310 for use in performing DNA sequencereconstruction using light energy exciter 10 is described in theflowchart of FIG. 20.

At block 1802 process control system 310 can clear flow cell 282,meaning process control system 310 can remove fluid from flow cell 282used during a prior cycle. At block 1804, process control system 310 caninput into flow cell 282 fluid having multiple fluorophores, e.g. firstand second fluorophores, or first, second and third fluorophores. Thefirst and second fluorophores can include, e.g. the absorptioncharacteristics described with reference to absorption band spectralprofile 1704 and absorption band spectral profile 1714 respectively asdescribed in reference to the spectral profile diagram of FIG. 19. Firstsecond and third fluorophores can include, e.g. the absorptioncharacteristics described with reference to absorption band spectralprofile 1704 and absorption band spectral profile 1714 and absorptionband spectral profile 1707 respectively as described in reference to thespectral profile diagram of FIG. 19.

At block 1806, process control system 310 can read out signals fromlight sensors 202 exposed with a first wavelength range excitationactive. At block 1806, process control system 310 can control lightenergy exciter 10 so that during an exposure period of light sensors 202light energy exciter 10 emits excitation light restricted excitation byone or more green light sources. At block 1806, process control system310 can during an exposure period of light sensors 202 energize each oneor more green emitting light sources of light source bank 102, e.g.light sources 102A-102G as set forth in FIG. 4, while maintaining in adeenergized state each one or more blue emitting light sources of lightbank, e.g. light sources 102H-102J as set forth in FIG. 4. With thelight source bank 102 being controlled as described so that green lightsources are on and blue light sources are off during an exposure periodof light sensors 202, process control system 310 at block 1806 can readout first signals from light sensors 202 exposed with excitationrestricted to excitation by one or more green light sources as set forthherein.

At block 1808, process control system 310 can read out signals fromlight sensors 202 exposed with a second wavelength range excitationactive. At block 1808, process control system 310 can control lightenergy exciter 10 so that during an exposure period of light sensors 202light energy exciter 10 emits excitation light restricted to excitationby one or more blue light sources of light energy exciter 10. At block1808, process control system 310 can during an exposure period of lightsensors 202 energize each of one or more blue emitting light sources oflight source bank 102, e.g. light sources 102H-102J as set forth in FIG.4, while maintaining in a deenergized state each one or more greenemitting light sources of light bank, e.g. light sources 102A-102G asset forth in FIG. 4. With the light source bank 102 being controlled asdescribed so that blue light sources are on and green light sources areoff during an exposure period of light sensors 202, process controlsystem 310 at block 1808 can read out second signals from light sensors202 exposed with excitation restricted to excitation by one or more bluelight sources as set forth herein.

At block 1810 process control system 310 for the current cycle canprocess the first signals read out at block 1806 and the second signalsread out at block 1808 to determine a nucleotide type of the DNAfragment being subject to testing during the current cycle, e.g. using adecision data structure as set forth in Table 2 according to oneexample. Process control system 310 can perform the described nucleotideidentification process described with reference to the flowchart of FIG.20 for each cycle of the DNA sequencing process until nucleotideidentification is performed for each scheduled cycle.

Process control system 310 can be configured to perform a wide range oftests for testing operation of the system 100. Process control system310 can perform a calibration test in which operation of light energyexciter 10 and detector 200 is tested. In such an example processcontrol system 310 can be configured to selectively energize differentlights sources during exposure periods of sensor array 201 and canexamine signals read out of sensor array 201 during the exposureperiods. A method can include selectively energizing a first lightsource (e.g. green emitting) during a first exposure period of the lightsensors with second (blue emitting) and third (e.g. red emitting) lightsources maintained in a deenergized state, selectively energizing thesecond light source during a second exposure period of the light sensorswith the first and third light sources maintained in a deenergizedstate, and selectively energizing the third light source during a thirdexposure period of the light sensors with the first and second lightsources maintained in a deenergized state.

It should be appreciated that all combinations of the foregoing conceptsand additional concepts discussed in greater detail below (provided suchconcepts are not mutually inconsistent) are contemplated as being partof the subject matter disclosed herein. In particular, all combinationsof claims subject matter appearing at the end of this disclosure arecontemplated as being part of the subject matter disclosed herein. Itshould also be appreciated that terminology explicitly employed hereinthat also may appear in any disclosure incorporated by reference shouldbe accorded a meaning most consistent with the particular conceptsdisclosed herein.

This written description uses examples to disclose the subject matter,and also to enable any person skilled in the art to practice the subjectmatter, including making and using any devices or systems and performingany incorporated methods. The patentable scope of the subject matter isdefined by the claims, and may include other examples that occur tothose skilled in the art. Such other examples are intended to be withinthe scope of the claims if they have structural elements that do notdiffer from the literal language of the claims, or if they includeequivalent structural elements with insubstantial differences from theliteral languages of the claims.

It is to be understood that the above description is intended to beillustrative, and not restrictive. For example, the above-describedexamples (and/or aspects thereof) may be used in combination with eachother. In addition, many modifications may be made to adapt a particularsituation or material to the teachings of the various examples withoutdeparting from their scope. While the dimensions and types of materialsdescribed herein are intended to define the parameters of the variousexamples, they are by no means limiting and are merely exemplary. Manyother examples will be apparent to those of skill in the art uponreviewing the above description. The scope of the various examplesshould, therefore, be determined with reference to the appended claims,along with the full scope of equivalents to which such claims areentitled. In the appended claims, the terms “including” and “in which”are used as the plain-English equivalents of the respective terms“comprising” and “wherein.” Moreover, in the following claims, the terms“first,” “second,” and “third,” etc. are used merely as labels, and arenot intended to impose numerical requirements on their objects. Forms ofterm “based on” herein encompass relationships where an element ispartially based on as well as relationships where an element is entirelybased on. Forms of the term “defined” encompass relationships where anelement is partially defined as well as relationships where an elementis entirely defined. Further, the limitations of the following claimsare not written in means-plus-function format and are not intended to beinterpreted based on 35 U.S.C. § 112, sixth paragraph, unless and untilsuch claim limitations expressly use the phrase “means for” followed bya statement of function void of further structure. It is to beunderstood that not necessarily all such objects or advantages describedabove may be achieved in accordance with any particular example. Thus,for example, those skilled in the art will recognize that the systemsand techniques described herein may be embodied or carried out in amanner that achieves or optimizes one advantage or group of advantagesas taught herein without necessarily achieving other objects oradvantages as may be taught or suggested herein.

While the subject matter has been described in detail in connection withonly a limited number of examples, it should be readily understood thatthe subject matter is not limited to such disclosed examples. Rather,the subject matter can be modified to incorporate any number ofvariations, alterations, substitutions or equivalent arrangements notheretofore described, but which are commensurate with the spirit andscope of the subject matter. Additionally, while various examples of thesubject matter have been described, it is to be understood that aspectsof the disclosure may include only some of the described examples. Also,while some examples are described as having a certain number of elementsit will be understood that the subject matter can be practiced with lessthan or greater than the certain number of elements. Accordingly, thesubject matter is not to be seen as limited by the foregoingdescription, but is only limited by the scope of the appended claims.

1. A method comprising: emitting with a light energy exciter excitationlight, wherein the light energy exciter comprises a first light sourceand a second light source, the first light source to emit excitationlight rays in a first wavelength emission band, the second light sourceto emit excitation light rays in a second wavelength emission band;receiving with a detector the excitation light and emissions signallight resulting from excitation by the excitation light, the detectorcomprising a detector surface for supporting biological or chemicalsamples and a sensor array spaced apart from the detector surface, thedetector blocking the excitation light and permitting the emissionssignal light to propagate toward light sensors of the sensor array; andtransmitting with circuitry of the detector data signals in dependenceon photons sensed by the light sensors of the sensor array.
 2. Themethod of claim 1, wherein the emitting with a light energy exciterincludes imaging a light pipe light exit surface of the light energyexciter to project an illumination pattern that matches a size and shapeof the detector surface.
 3. The method of claim 1, wherein the methodincludes fabricating the detector using complementary metal oxidesemiconductor (CMOS) integrated circuit fabrication technology.
 4. Themethod of claim 1, wherein the method comprises for each of a pluralityof cycles in support of a DNA sequencing process (a) removing fluid froma flow cell defined by the detector surface, (b) filling the flow cellwith first and second dyes so that first and second dyes aresimultaneously contained within the flow cell, and (c) reading out firstsignals from the light sensors exposed to emissions signal light withthe first light source energized and the second light source maintainedin a deenergized state, (d) reading out second signals from the lightsensors exposed to emissions signal light with the second light sourceenergized and the first light source maintained in a deenergized state,and (e) identifying a DNA nucleotide using signals of the first signalsand signals of the second signals.
 5. The method of claim 1, wherein thelight energy exciter comprises a third light source to emit light in athird wavelength emission band, wherein the emitting includesselectively energizing the first light source during a first exposureperiod of the light sensors with the second light source and the thirdlight source maintained in a deenergized state, wherein the emittingcomprises selectively energizing the second light source during a secondexposure period of the light sensors with the first light source and thethird light source maintained in a deenergized state, wherein theemitting comprises selectively energizing the third light source duringa third exposure period of the light sensors with the first light sourceand the second light source maintained in a deenergized state.
 6. Alight energy exciter comprising: at least one light source to emitexcitation light rays; and a light pipe homogenizing the excitationlight and directing the excitation light toward a distal end of thelight energy exciter, the light pipe comprising a light entrance surfaceand a light exit surface, the light pipe receiving the excitation lightrays from the at least one light source; wherein the distal end of thelight energy exciter is adapted for coupling with a detector assemblythat comprises a detector surface for supporting biological or chemicalsamples.
 7. The light energy exciter of claim 6, wherein the distal endof the light energy exciter comprises a shaped housing portion adaptedfor fitting into a correspondingly shaped housing portion of thedetector assembly.
 8. The light energy exciter of claim 6, wherein thelight energy exciter comprises a lens that images an object planedefined by the light exit surface onto an image plane defined by adetector surface of the detector assembly when the distal end of thelight energy exciter is coupled to the detector assembly.
 9. The lightenergy exciter of claim 6, wherein the at least one light sourcecomprises a light emitting diode that is surface coupled to the lightentrance surface of the light pipe.
 10. The light energy exciter ofclaim 6, wherein the at least one light source comprises first andsecond light sources, wherein the light receives excitation light raysfrom the light source, and wherein the light energy exciter comprises asecond light pipe housed in a common housing with the light pipe,wherein the second light pipe receives excitation light rays from thesecond light source, wherein the light pipe and the second light pipepropagate the excitation light rays emitted from the first light sourceand the second light source, respectively, and wherein the light energyexciter shapes the excitation light rays propagating, respectively,through the light pipe and the second light pipe to define first andsecond separate illumination patterns.
 11. The light energy exciter ofclaim 6, wherein the at least one light source comprises a first lightemitting diode that is surface coupled to the light entrance surface ofthe light pipe, and a second light emitting diode that is surfacecoupled to the light entrance surface of the light pipe, the first lightemitting diode to emit light in a first wavelength band, the secondlight emitting diode to emit light in a second wavelength band.
 12. Thelight energy exciter of claim 6, wherein the light pipe is of taperedconstruction and comprises an increasing diameter, in a direction fromthe light entry surface of the light pipe to the light exit surface ofthe light pipe, throughout a length of the light pipe, the light pipereflecting the excitation light so that light pipe exit light raysexiting the light exit surface of the light pipe define a diverging coneof light that diverges with respect to an optical axis of the lightenergy exciter.
 13. The light energy exciter of claim 6, wherein thelight pipe is of tapered construction and comprises an increasingdiameter, in a direction from the light entry surface of the light pipeto the light exit surface of the light pipe, throughout a length of thelight pipe of the light pipe, the light pipe reflecting the excitationlight so that exit light rays exiting the light exit surface of thelight pipe define a diverging cone of light that diverges with respectto an optical axis of the light energy exciter, wherein the exit lightrays diverge at angles ranging from zero degrees to a maximum divergenceangle in respect to a reference light ray extending from the light exitsurface in a direction parallel to the optical axis, wherein the maximumdivergence angle is an angle of less than about 60 degrees.
 14. Thelight energy exciter of claim 6, wherein the light pipe is of taperedconstruction and comprises an increasing diameter, in a direction fromthe light entry surface of the light pipe to the light exit surface,throughout a length of the light pipe of the light pipe, the light pipereflecting the excitation light so that light pipe exit light raysexiting the light exit surface of the light pipe define a diverging coneof light that forms an angle with respect to an optical axis that isreduced relative to a diverging cone of light divergence angle formedwithout the tapered construction.
 15. The light energy exciter of claim6, wherein the light energy exciter comprises a lens that receives theexcitation light from the light pipe and shapes light rays of theexcitation light so that excitation light rays of the excitation lightexiting the distal end of the light energy exciter define a convergingcone of light that converges toward an optical axis of the light energyexciter to project an illumination pattern matching a size and shape ofthe detector surface.
 16. The light energy exciter of claim 6, whereinthe light energy exciter comprises a lens that receives the excitationlight from the light pipe and shapes light rays of the excitation lightso that excitation light rays exiting a light exit surface of the lensdefine a converging cone of light that converges toward an optical axisof the light energy exciter, wherein the light exit rays exiting thelens converge at angles ranging from zero degrees to a maximumconvergence angle in respect to a reference light ray extending from thelight exit surface in a direction parallel to the optical axis, whereinthe maximum divergence angle is an angle of less than about 60 degrees.17. The light energy exciter of claim 6, wherein the at least one lightsource comprises a light emitting diode that is surface coupled to thelight entrance surface of the light pipe, wherein the light pipecomprises glass, wherein the light pipe is of tapered construction andcomprises an increasing diameter, in a direction from the light entrysurface of the light pipe to the light exit surface, throughout a lengthof the light pipe of the light pipe, the light pipe reflecting theexcitation light so that light pipe exit light rays exiting the lightexit surface of the light pipe define a diverging cone of lightdiverging with respect to an optical axis of the light energy exciter,wherein the light energy exciter comprises a lens that receives theexcitation light from the light pipe and shapes light rays of theexcitation light so that light rays of the excitation light exiting thedistal end of the light energy exciter define a converging cone of lightthat converges with respect to the optical axis of the light energyexciter, wherein the light energy exciter comprises one or more filtersto filter light at wavelengths longer than a cumulative emission band ofwavelengths of the one or more light sources, and wherein the lightenergy exciter comprises folding optics folding the optical axis.
 18. Asystem comprising: a light energy exciter comprising at least one lightsource to emit excitation light rays, and a light pipe to homogenize theexcitation light rays and to direct the excitation light rays, the lightpipe comprising a light entrance surface to receive the excitation lightrays from the at least one light source; and a detector comprising adetector surface for supporting biological or chemical samples and asensor array comprising light sensors spaced apart from the detectorsurface, wherein the detector receives excitation light from the exciterand emissions signal light, wherein the detector comprises circuitry totransmit data signals in dependence on photons detected by light sensorsof the sensor array, wherein the detector blocks the excitation lightand permits the emissions signal light to propagate toward the lightsensors.
 19. The system of claim 18, wherein the light energy excitercomprises a lens focusing an object plane defined by a light exitsurface of the light pipe onto an image plane defined by the detectorsurface.
 20. The system of claim 18, wherein the at least one lightsource comprises a light emitting diode that is surface coupled to thelight entrance surface of the light pipe, wherein the light pipecomprises glass, wherein the light pipe is of tapered construction andcomprises an increasing diameter, in a direction from the light entrysurface of the light pipe to a light exit surface of the light pipe,throughout a length of the light pipe, the light pipe reflectingexcitation light so that light pipe exit light rays exiting the lightexit surface of the light pipe define a diverging cone of light thatdiverges with respect to an optical axis of the light energy exciter,wherein the light energy exciter comprises a lens that receives theexcitation light from the light pipe and shapes light rays of theexcitation light so that light exit light rays exiting the lens define aconverging cone of light that converges with respect to an optical axisof the light energy exciter, wherein the light energy exciter comprisesone or more filters to filter light at wavelengths longer than acumulative emission band of wavelengths of the one or more lightsources.